The waiting time before starting a program is part of the bootloader program, so you will need to change the bootloader in order to remove it or change it and re-program the modified bootloader in your board using an AVRISP or similar ISP dongle to do it (the ISP connector in the board is used for that). Please check the bootloader source code here: http://wiring.uniandes.edu.co/source/trunk/wiring/bootloader/